Genome confirms the origin of string beans

The common bean is thought to have originated in Mexico more than 100,000 years ago, but was actually domesticated separately at two different geographic locations in Mesoamerica and the southern Andes, says Paul Gepts. "This finding makes the common bean an unusually interesting experimental system because the domestication process has been replicated in this crop." (Credit: Andreas Winterer/Flickr)

“The availability of this new whole-genome sequence for beans is already paying off,” says Paul Gepts, a plant scientist at University of California, Davis, who leads the bean-breeding program and is responsible for producing new varieties of common beans and lima and garbanzo beans.

Researchers are using the new sequence to confirm many earlier findings, including to identify the common bean’s two points of origin and domestication—one in the Andes and the other in the Mesoamerican area of Central America.

They also are working to identify genetic markers that will speed up efforts to breed new bean varieties in the United States, East Africa, and other countries.

The nitrogen connection

The common bean, Phaseolus vulgaris, includes kidney, navy, string, and pinto beans. All of these well-known bean varieties share with the closely related soybean the highly valued ability to form symbiotic relationships with “nitrogen-fixing” bacteria in the soil.

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Working together, the plants and bacteria convert nitrogen in the atmosphere into ammonia—which includes nitrogen in a form that enriches the soil and feeds crops. Nitrogen-fixing crop plants can actually reduce or eliminate the need for farmers to apply expensive fertilizers.

One of the goals of the sequencing project was to better understand the genetic basis for how such symbiotic relationships between nitrogen-fixing plants and bacteria are formed and sustained. This will be critically important for increasing crop yields for both fuel and food production.

The new sequencing identified a handful of genes involved with moving nitrogen around, which could be helpful to farmers who intercrop beans with other crops that don’t fix nitrogen.

Bean and soybeans

The common bean is thought to have originated in Mexico more than 100,000 years ago, but was actually domesticated separately at two different geographic locations in Mesoamerica and the southern Andes.

“This finding makes the common bean an unusually interesting experimental system because the domestication process has been replicated in this crop,” Gepts says.

The sequencing team compared gene sequences from pooled populations of plants representing these two regions and found that only a small fraction of the genes are shared between common bean species from the two locations. This supports the earlier finding that the common bean was domesticated in two separate events, one at each location, but distinct genes were involved in each event.

The researchers also discovered:

Dense clusters of genes related to disease resistance within the common bean’s chromosomes

Certain genes that are shared by both the common bean and the soybean, its most economically important relative

Evidence that the common bean’s genome evolved more rapidly than did the soybean genome, after the two species parted ways on the evolutionary pathway nearly 20 million years ago

The project was led by researchers at the University of Georgia, US Department of Energy Joint Genome Institute, Hudson Alpha Institute for Biotechnology, and North Dakota State University. The US Department of Energy and Department of Agriculture funded the research, which was detailed in an article published in Nature Genetics.